The potential impact of climate change was investigated on the hydrology and hydrological extremes of Nyando River and Lake Tana catchments, located in two source regions of the Nile River basin. Climate change scenarios were developed for rainfall and potential evapotranspiration (ETo), considering 17 different General Circulation Model (GCM) simulations to better understand the range of possible future change. Projected changes under two future emission scenarios for the 2050s were extracted from an ensemble of selected GCM experiments. The future climate change scenarios were constructed by transferring the extracted climate change signals to the observed series using a frequency perturbation downscaling approach, which accounts for the effect on rainfall and ETo extremes, its dependence on the return period of rain storm depth, and the correlation between rainfall and ETo changes. Two conceptual hydrological models were calibrated and used for the impact assessment. Their difference in simulating the flows under future climate scenarios was investigated. The results reveal that the hydrological models project increasing runoff extremes for Nyando catchment towards the 2050s while unclear trend is observed for Lake Tana catchment for cumulative volumes as well as high and low flows.